Evaluate gene sets by cell type-specific gene expression
Wei Sun
2024-07-04
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 2.00 21.00 22.00 20.98 22.00 23.00## [1] 40## [1] 2 18 19 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22 22 22
## [26] 22 22 22 22 22 22 22 22 22 23 23 23 23 23 23Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"##
## FALSE TRUE
## 1607 42##
## FALSE TRUE <NA>
## 42 1565 42gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: C10orf91 LINC02870
## 2: C12orf10 MYG1
## 3: C12orf45 NOPCHAP1
## 4: C6orf48 SNHG32
## 5: C6orf99 LINC02901
## 6: CXorf40A EOLA1
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM173A ANTKMT
## 10: FAM213B PRXL2B
## 11: H2AFX H2AX
## 12: HIST1H2AG H2AC11
## 13: HIST1H2BK H2BC12
## 14: HIST1H2BN H2BC15
## 15: HIST1H3A H3C1
## 16: HIST1H3H H3C10
## 17: HIST1H4C H4C3
## 18: HIST2H2BF H2BC18
## 19: KIAA0391 PRORP
## 20: QARS EPRS1
## 21: SEPT6 SEPTIN6
## 22: ARNTL BMAL1
## 23: C12orf65 MTRFR
## 24: C16orf72 HAPSTR1
## 25: CCDC84 CENATAC
## 26: DOPEY2 DOP1B
## 27: FAM126B HYCC2
## 28: FAM160B1 FHIP2A
## 29: H1FX H1-10
## 30: H2AFJ H2AJ
## 31: HEXDC HEXD
## 32: HIST1H1C H1-2
## 33: HIST1H1D H1-3
## 34: HIST1H1E H1-4
## 35: KIAA1109 BLTP1
## 36: KIAA1551 RESF1
## 37: MKL1 MRTFA
## 38: NARFL CIAO3
## 39: SEPT2 SEPTIN6
## 40: TARSL2 TARS3
## 41: TMEM8A PGAP6
## 42: WDR60 DYNC2I1
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 1649 3## sym_in_data sym_limma gene_symbol
## 1: ABLIM1 ABLIM1 ABLIM1
## 2: AC004687.1 <NA> AC004687.1
## 3: AC004854.2 <NA> AC004854.2
## 4: AC007384.1 <NA> AC007384.1
## 5: AC007952.4 <NA> AC007952.4## t1
## 1 2
## 1647 1## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6Read in cell type-specific expression data
Cell type specific gene expression were downloaded from protein atlas.
## [1] 1587110 4## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5## [1] 79##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090## [1] 602700 5## Gene Gene name Immune cell TPM pTPM
## 1: ENSG00000000003 TSPAN6 basophil NA 1.2
## 2: ENSG00000000003 TSPAN6 Central memory CD8 T-cell NA 1.7
## 3: ENSG00000000003 TSPAN6 classical monocyte NA 0.2
## 4: ENSG00000000003 TSPAN6 Effector memory CD8 T-cell NA 0.7
## 5: ENSG00000000003 TSPAN6 Exhausted memory B-cell NA 0.7## Mode NA's
## logical 602700## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 0.00 3.10 49.74 27.20 96572.50## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.10 1.70 11.60 67.96 42.80 96572.50## [1] 30##
## basophil Central memory CD8 T-cell
## 20090 20090
## classical monocyte Effector memory CD8 T-cell
## 20090 20090
## Exhausted memory B-cell intermediate monocyte
## 20090 20090
## MAIT T-cell Memory CD4 T-cell TFH
## 20090 20090
## Memory CD4 T-cell Th1 Memory CD4 T-cell Th1/Th17
## 20090 20090
## Memory CD4 T-cell Th17 Memory CD4 T-cell Th2
## 20090 20090
## myeloid DC naive B-cell
## 20090 20090
## naive CD4 T-cell naive CD8 T-cell
## 20090 20090
## neutrophil NK-cell
## 20090 20090
## non-classical monocyte Non-switched memory B-cell
## 20090 20090
## Non-Vd2 gdTCR Plasmablast
## 20090 20090
## plasmacytoid DC Progenitor cell
## 20090 20090
## Switched memory B-cell T-reg
## 20090 20090
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell
## 20090 20090
## total PBMC Vd2 gdTCR
## 20090 20090## [1] 30 2## Cell_type Lineage
## 1: Basophil Granulocytes
## 2: Neutrophil GranulocytesCheck gene expression for each gene set
## [1] 1649 3for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct_immune$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct_immune[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Immune cell`) %in%
str_to_lower(lineage$Cell_type)))
mat1 = match(str_to_lower(df$`Immune cell`),
str_to_lower(lineage$Cell_type))
df = cbind(df, lineage[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
df = df[df$Lineage != "Total PBMC",]
df$Lineage = factor(df$Lineage,
levels = setdiff(lineage$Lineage, "Total PBMC"))
p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "CD83" "RHOC" "RPL41" "TLE4" "ASCL2" "CD226" "GNLY" "MKLN1"
## [9] "PLAC8" "PRR5L" "PTPN4" "SPN" "THADA" "TMSB10" "TMSB4X" "UVRAG"
## [17] "VPS18" "VPS39" "XPO6" "YPEL5" "ZZEF1"
## [1] "found 21 genes."
## [1] 2
## [1] "DTHD1" "GSTM1" "NT5DC1" "SLC27A5" "SLC4A4" "TRAV8-4" "ZNF862"
## [8] "ADCY7" "ARAP2" "BICRAL" "DIAPH2" "DMTF1" "GPR141" "MCTP2"
## [15] "MIAT" "MTERF2" "MYBL1" "NFATC3" "NLRC3" "TUT7" "UNC13D"
## [22] "XIST" "ZNF83"
## [1] "found 21 genes."
## [1] 3
## [1] "APMAP" "CD84" "CMC1" "FAM118A" "FCER1G" "ICAM3"
## [7] "KLRF1" "KLRG1" "LEPROTL1" "LETMD1" "LRRC23" "NCR1"
## [13] "RTN3" "SH2D1A" "THAP9-AS1" "TMEM107" "TMEM42" "MCOLN2"
## [19] "PATL2" "PCSK7" "RASA3" "SLFN5"
## [1] "found 21 genes."
## [1] 4
## [1] "ARHGAP9" "CYB5D2" "HLA-DMB" "INTS8" "KLRB1" "MZT2A"
## [7] "PDE3B" "RCSD1" "ABCC1" "AHCTF1" "DOPEY2" "ENTPD4"
## [13] "HLA-DQA1" "KLRD1" "LPCAT1" "PNPLA6" "PTPN7" "SLC38A10"
## [19] "ST6GAL1" "TAP2" "UGGT1"
## [1] "found 21 genes."
## [1] 5
## [1] "ACTR1B" "ATP5MG" "COQ7" "CPNE1" "FAM102A" "GLRX5"
## [7] "MARCKSL1" "MPST" "NMT2" "RACK1" "UIMC1" "WDR86"
## [13] "DNAJB14" "GDPD5" "HERC3" "HERC6" "KIAA0232" "NUP210"
## [19] "R3HCC1L" "ZNF335" "ZNF800"
## [1] "found 20 genes."
## [1] 6
## [1] "AC245297.3" "AL139246.5" "BBS9" "CRTAM" "CXorf57"
## [6] "EOMES" "HIST1H3H" "MFNG" "NUAK2" "PITPNC1"
## [11] "TRAV12-2" "TRAV38-2DV8" "TRBV3-1" "TRBV6-2" "TRBV6-5"
## [16] "CYTOR" "FAM126B" "GK5" "GPR174" "NRDC"
## [21] "OGA" "PARP15" "PIK3R5"
## [1] "found 19 genes."
## [1] 7
## [1] "NUCB2" "PAIP2" "PDLIM1" "PTGER4" "RPL22L1" "STMN3"
## [7] "CWC25" "DENND4C" "GIGYF1" "GPANK1" "HELZ" "KIF13B"
## [13] "L3HYPDH" "MAN2C1" "RNMT" "SCAF8" "SECISBP2" "TIMP1"
## [19] "ZCCHC2"
## [1] "found 19 genes."
## [1] 8
## [1] "C10orf91" "ANKRD36B" "ANKRD36C" "C16orf72" "CD46" "CHD9"
## [7] "CROCC" "DGKD" "EML4" "MIGA1" "RNF19A" "RPS6KA5"
## [13] "RSAD2" "RUBCN" "STAT4" "STK10" "SYNE1" "UBE2H"
## [19] "UBR2" "VPS13C" "ZNF493" "ZNF708"
## [1] "found 20 genes."
## [1] 9
## [1] "ALOX5AP" "HDHD3" "KLRK1" "MATK" "TMEM134" "ANKRD12" "BTBD9"
## [8] "CST7" "GZMA" "GZMB" "IRF9" "KLF3" "LILRB1" "MYO1F"
## [15] "NKG7" "RNF125" "SPON2" "SRGN" "TMEM181" "UCP2" "ZFAND3"
## [1] "found 21 genes."
## [1] 10
## [1] "AC008555.5" "AC044849.1" "AC083798.2" "AL135791.1" "COQ8A"
## [6] "FAM213B" "HIKESHI" "MTRNR2L8" "NBPF14" "PCMTD2"
## [11] "PRAG1" "RGL4" "TOX" "TRAV13-1" "TRAV14DV4"
## [16] "TRAV5" "TRBV7-2" "TRBV7-9" "TRGV5" "TRGV7"
## [21] "WARS2" "ZNF749"
## [1] "found 17 genes."
## [1] 12
## [1] "BTG1" "HIST1H4C" "ID2" "JADE1" "LDLRAP1" "MSC"
## [7] "PNRC1" "WDR54" "ZNF575" "ARRDC3" "BRPF1" "COX19"
## [13] "GCN1" "GON4L" "KAT6B" "MAPK8IP3" "PHF14" "PKD1"
## [19] "RORA" "USP16" "ZNF292"
## [1] "found 21 genes."
## [1] 13
## [1] "AC004687.1" "AC004854.2" "AC015982.1" "AC020911.2" "AC083880.1"
## [6] "AC091271.1" "AC103591.3" "AF213884.3" "AL357060.1" "AL451085.1"
## [11] "AL627171.1" "ARF4-AS1" "ATP2B1-AS1" "C6orf99" "HELQ"
## [16] "HIPK1-AS1" "KCNQ1OT1" "LINC01465" "MZF1-AS1" "OSER1-DT"
## [21] "PGGHG" "NEK9"
## [1] "found 3 genes."
## [1] 14
## [1] "AOAH" "CCL4L2" "TRAV3" "TRG-AS1" "TRGV8" "TRGV9"
## [7] "CARD11" "CARD16" "EPSTI1" "FCRL6" "FGL2" "ITM2A"
## [13] "LINC02384" "NECAP1" "PTPRJ" "TRAV9-2" "TRDC" "TRDV1"
## [19] "TRGC2" "TRGV4" "TTC38" "XCL2"
## [1] "found 19 genes."
## [1] 15
## [1] "ASAH1" "COMMD6" "COTL1" "ITGB1BP1" "LAPTM5" "NSUN6"
## [7] "PTPRCAP" "TPGS2" "CCNH" "CD2" "CD52" "CD8A"
## [13] "CD8B" "ITK" "LY6E" "PRSS23" "RHOH" "SBK1"
## [19] "SLC35F5" "TRAC" "TRBC2" "ZDHHC20"
## [1] "found 22 genes."
## [1] 16
## [1] "TPRKB" "BDP1" "CHD1" "DHX29" "HELZ2" "HEXDC" "IFI44"
## [8] "IFIT2" "IFIT3" "KLHDC4" "MSI2" "MX1" "NEMF" "OAS3"
## [15] "PHACTR4" "PLA2G6" "REXO1" "RNF157" "RNPC3" "SPOCK2" "VAV3"
## [22] "ZC3H7B"
## [1] "found 22 genes."
## [1] 17
## [1] "IL6R" "SERINC5" "TRBV6-1" "ABCA5" "ABR"
## [6] "AC020659.1" "CCDC84" "CPPED1" "DDX3Y" "EIF1AY"
## [11] "ENOSF1" "IL6ST" "KDM5D" "MICAL2" "OSM"
## [16] "RPS4Y1" "SBNO2" "SIDT1" "TRBV4-2" "ZMIZ2"
## [21] "ZNF236" "ZNF652"
## [1] "found 21 genes."
## [1] 18
## [1] "ARHGAP45" "CEMIP2" "CRYBG1" "FAM133B" "MX2"
## [6] "OAS2" "PIK3CD" "PPP4R3B" "PREX1" "PUM3"
## [11] "RIPOR2" "S100A12" "SAMD9L" "TENT5C" "THUMPD3-AS1"
## [16] "TMEM131L" "TRANK1" "TRAV19" "TRAV27" "TRBV11-2"
## [21] "TRBV2" "TUT4"
## [1] "found 20 genes."
## [1] 19
## [1] "AMD1" "CD27" "CREBL2" "CYB561A3" "EI24" "GIMAP1"
## [7] "GLTP" "IER3" "IFRD1" "KIR3DL2" "LIME1" "MZF1"
## [13] "NELL2" "PDE7A" "PPP1R15B" "SLC38A1" "TMEM204" "TSPYL4"
## [19] "LTBP4" "TRIM38" "VPS13A" "ZBTB40"
## [1] "found 22 genes."
## [1] 20
## [1] "RGCC" "ACOX1" "BTN3A1" "CAST" "CCDC88C" "CELF2"
## [7] "DDHD1" "KDM5A" "MTMR6" "NCKAP1L" "NLRC5" "PCYT1A"
## [13] "PRKCH" "RAP1GAP2" "RASGRP1" "SPG11" "SYNRG" "TAOK1"
## [19] "TAOK3" "TIPARP" "ZEB2"
## [1] "found 21 genes."
## [1] 21
## [1] "ID1" "RGS1" "AC092683.1" "AP005482.1" "ATAD2B"
## [6] "BMT2" "DOCK10" "ETFDH" "FAM78A" "GABPB2"
## [11] "GRK2" "HRH2" "IGKV3-15" "LINC02256" "MARF1"
## [16] "MINDY2" "NBEAL2" "POLR2J3-1" "SEC14L1" "THAP5"
## [21] "Z93930.2" "ZNF808"
## [1] "found 17 genes."
## [1] 22
## [1] "ARL4A" "ABCA7" "CAPNS1" "ELMO1" "ERICH1" "FAM53B"
## [7] "FNBP1" "HSH2D" "IFI44L" "IL2RG" "IRAK4" "KCNAB2"
## [13] "KIAA1551" "KIAA2026" "KLF6" "PNPLA8" "PRDM2" "SENP7"
## [19] "TTC14" "WASL" "XAF1"
## [1] "found 21 genes."
## [1] 23
## [1] "AC012645.3" "AC027644.3" "AC087623.3" "AK5" "AL118516.1"
## [6] "BX284668.6" "CHRM3-AS2" "FXYD7" "IGLV1-44" "INTS6L"
## [11] "KMT2E-AS1" "LINC00402" "LINC00649" "LST1" "MAP3K2"
## [16] "MATR3-1" "PDCD4-AS1" "RETREG1" "SNHG15" "TRAV21"
## [21] "TRAV8-2" "TRAV8-3"
## [1] "found 10 genes."
## [1] 24
## [1] "C12orf45" "CAMK4" "CRLF3" "GCH1" "PLK2" "ZNF10"
## [7] "ANKRD44" "EHMT1" "FRYL" "MBD5" "PIGF" "POLH"
## [13] "PPP6R2" "PRR14L" "RLF" "SETD2" "SETX" "SP3"
## [19] "USP34" "WDR7" "ZNF407"
## [1] "found 20 genes."
## [1] 25
## [1] "AL136454.1" "ATP5F1A" "CCNI" "COA1" "EFCAB2"
## [6] "FAM173A" "FCMR" "FCRL3" "GCSAM" "GTF3A"
## [11] "ITGAE" "RTRAF" "TRBC1" "ADGRE5" "ARHGAP30"
## [16] "CD38" "CTSW" "IFITM2" "MT2A" "MYO1G"
## [21] "SLA2" "ZNF683"
## [1] "found 21 genes."
## [1] 26
## [1] "AIF1" "CD28" "YPEL3" "ANKRD49" "CASP10" "CFLAR"
## [7] "ETNK1" "FNDC3B" "GCA" "GPATCH2L" "H6PD" "IGHA1"
## [13] "LSS" "NCOA7" "PHF11" "PRKX" "PTGDS" "SETD5"
## [19] "WDTC1"
## [1] "found 19 genes."
## [1] 27
## [1] "GNAQ" "NXT2" "AC016831.7" "ADHFE1" "AKNA"
## [6] "APOL6" "ARL4C" "ELMOD3" "GBP1" "GBP5"
## [11] "GNPTAB" "GPR132" "IFI27" "INPP4A" "ISG20"
## [16] "PDZD4" "PPP1R16B" "RAB27B" "SLFN12L" "SYTL3"
## [21] "TTC16"
## [1] "found 20 genes."
## [1] 28
## [1] "BTG2" "C12orf10" "C12orf57" "CCNL1" "GSTM4" "KCTD7"
## [7] "MAP3K8" "MAPRE2" "NELFCD" "NEU1" "PTRHD1" "RPS26"
## [13] "RSRP1" "SEPT6" "SMDT1" "TGIF1" "ZFP36L1" "ACAP3"
## [19] "PARP4" "TEP1"
## [1] "found 20 genes."
## [1] 29
## [1] "AC016405.3" "AC087239.1" "AC245014.3" "ANXA2R" "CITED2"
## [6] "CSKMT" "CXorf40A" "IER5" "IGKV3-20" "ILF3-DT"
## [11] "NOCT" "PIK3IP1" "SDR42E2" "SLC2A3" "SLC38A2"
## [16] "STK17A" "TC2N" "TRBV28" "WSB1" "Z93241.1"
## [21] "ZFAS1" "MALAT1"
## [1] "found 15 genes."
## [1] 30
## [1] "BACH2" "CSRNP1" "EGR1" "EPS8" "FOSB" "MYLIP" "NOSIP" "NR1D1"
## [9] "NR4A2" "NR4A3" "RCAN3" "SELL" "SNHG12" "TCF7" "TXK" "CYTH1"
## [17] "DUS1L" "JUND" "MIDN" "SCRN3" "VCAN"
## [1] "found 20 genes."
## [1] 31
## [1] "ASL" "CLDND1" "CXXC5" "GATA3" "PAPSS1" "RAB33B" "SESN1"
## [8] "SESN2" "TBCCD1" "TIGIT" "CSNK1G2" "ERAP2" "GALNT3" "ITGAM"
## [15] "KIR2DL3" "PYROXD1" "RAPGEF1" "RUFY2" "SZT2" "TBX21" "VPS13B"
## [22] "YPEL1" "ZDHHC5"
## [1] "found 23 genes."
## [1] 32
## [1] "NT5E" "TBC1D17" "AFF1" "AFF4" "ARHGAP4" "BAZ2A" "CEP164"
## [8] "CRNKL1" "LRRFIP1" "LUC7L3" "NKTR" "PNN" "PPIG" "PPIL2"
## [15] "SRSF10" "SRSF11" "WDR60" "YTHDC1"
## [1] "found 18 genes."
## [1] 33
## [1] "ZC3H12A" "B4GALT1" "BCL9L" "C2CD3" "CAPN15" "EHBP1L1" "LONP2"
## [8] "LPIN1" "NAA25" "NFKBIZ" "PDE4B" "PDE4D" "PIM1" "RALGAPB"
## [15] "RIC3" "STK17B" "TBC1D2B" "TOB1" "UTY" "ZBTB20"
## [1] "found 20 genes."
## [1] 34
## [1] "GALNT11" "ADGRG1" "ARHGAP10" "CCL4" "CES1" "CX3CR1"
## [7] "ERBIN" "FGFBP2" "GALNT10" "GALNT2" "ITGAL" "LAG3"
## [13] "MPPE1" "MYO9B" "PEX1" "PEX26" "PLEK" "SEMA4D"
## [19] "ST8SIA4" "SUSD1" "TMEM8A"
## [1] "found 21 genes."
## [1] 35
## [1] "HMBOX1" "KIF9" "ANKRD36" "AP3B1" "AP3M2" "ARAP1" "ARID5B"
## [8] "ATG2A" "ATG2B" "CLEC16A" "CREBZF" "FAM13B" "GPRIN3" "HECTD4"
## [15] "INO80" "INO80D" "INPP5D" "KLF2" "MKL1" "NARFL" "NFE2L1"
## [22] "PIP4K2B" "ZNF557"
## [1] "found 23 genes."
## [1] 36
## [1] "AC025164.1" "AL121944.1" "AL138963.3" "ARMH1" "C6orf48"
## [6] "CCR7" "INPP4B" "JAML" "LINC02273" "LRRN3"
## [11] "LTB" "NPIPB4" "NUP58" "TCEA3" "TMIGD2"
## [16] "TNFRSF25" "TRABD2A" "TRAV1-2" "TRBV9" "OXNAD1"
## [21] "PARP11" "PCED1B"
## [1] "found 17 genes."
## [1] 37
## [1] "AC007952.4" "AC119396.1" "ALKBH7" "BNIP3L" "CD40LG"
## [6] "CMTM7" "DYRK4" "EPB41L4A-AS1" "EPHX2" "GADD45B"
## [11] "GZMK" "HIBADH" "MCUB" "NOP53" "RGS10"
## [16] "SNHG8" "TCP11L2" "TESPA1" "TRBV20-1" "ZFAND1"
## [21] "ITPR2" "LINC02446"
## [1] "found 17 genes."
## [1] 38
## [1] "CST3" "MAN2B1" "SAE1" "TRAT1" "ATP2B4" "CCDC112"
## [7] "CMKLR1" "CTSC" "DOCK11" "FAM169A" "LNPEP" "LRRC8A"
## [13] "PARP14" "RAB3GAP2" "SLC4A7" "SLK" "TMEM127" "TTC17"
## [19] "VPS13D" "ZNF276"
## [1] "found 20 genes."
## [1] 39
## [1] "ABCC10" "ARHGEF3" "COL6A2" "COL6A3" "DDX60L"
## [6] "DENND4B" "EIF4E3" "HECA" "HPS4" "LAIR2"
## [11] "N4BP1" "NUTM2B-AS1" "ODF3B" "SUSD6" "TRAV12-3"
## [16] "TRAV17" "TRAV4" "TRBV7-6" "TRGV10" "TSPAN32"
## [21] "TTTY15" "XCL1" "ZBP1"
## [1] "found 21 genes."
## [1] 40
## [1] "AC007384.1" "AC025171.3" "ARRDC2" "NT5C3B" "PRR7"
## [6] "SNHG9" "AC116407.2" "ARHGEF9" "BROX" "CHD6"
## [11] "DDIT4" "GPHN" "HIPK1" "IQCG" "KIAA1109"
## [16] "PCNX1" "PSMA3-AS1" "SLC16A1-AS1" "SLCO3A1" "SLF2"
## [21] "SPATA13" "TARSL2" "VTI1A"
## [1] "found 16 genes."
Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4184842 223.5 11673970 623.5 NA 11673970 623.5
## Vcells 20583330 157.1 61723001 471.0 65536 61693859 470.7## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5